head(NGS_rep_long)
## # A tibble: 6 x 11
## Sample Gene AA Var Sample_Var Run AF Mean_Sample_Var mean_minus_af
## <chr> <chr> <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl>
## 1 2079 EGFR R108K EGFR_~ 2079_EGFR~ 1st 0.052 0.0569 0.00486
## 2 2079 EGFR R108K EGFR_~ 2079_EGFR~ 2nd 0.058 0.0569 -0.00114
## 3 2079 EGFR R108K EGFR_~ 2079_EGFR~ 3rd 0.057 0.0569 -0.000143
## 4 2079 EGFR R108K EGFR_~ 2079_EGFR~ 4th 0.052 0.0569 0.00486
## 5 2079 EGFR R108K EGFR_~ 2079_EGFR~ 5th 0.06 0.0569 -0.00314
## 6 2079 EGFR R108K EGFR_~ 2079_EGFR~ 5th 0.059 0.0569 -0.00214
## # ... with 2 more variables: abs_mean_minus_af <dbl>, percent_dif <dbl>
ALL SAMPLES
Run vs Alele Frequency
p <- ggplot(data=NGS_rep_long, aes(Run, AF, group = Sample_Var, col = Sample_Var)) +
geom_point() +
geom_line() +
ggtitle("Run vs Allele Frequency: All Samples and Variants")
ggplotly(p)
Run Vs. Difference
p <- ggplot(data=NGS_rep_long, aes(Run, mean_minus_af, group = Sample_Var, col = Sample_Var)) +
geom_point() +
geom_line() +
geom_hline(yintercept = 0, linetype = "dashed", size = 0.2) +
ggtitle("Run vs (Mean AF - AF): All Samples and Variants") +
ylab("AF: Difference from Mean")
ggplotly(p)
Run vs % Difference
% Difference = ((difference/mean) * 100)
p <- ggplot(data=NGS_rep_long, aes(Run, percent_dif, group = Sample_Var, col = Sample_Var)) +
geom_point() +
geom_line() +
geom_hline(yintercept = 0, linetype = "dashed", size = 0.2) +
ggtitle("Run vs Percent Difference ((AF/Mean AF)*100): All Samples and Variants") +
ylab("AF: Percent Difference")
ggplotly(p)